Genomic Surveillance of Third-Generation Cephalosporin-Resistant <i>Klebsiella pneumoniae</i> in Tunisian AMR Surveillance System Hospitals

Abstract

Abstract Third-generation cephalosporin (3GC) resistant Klebsiella pneumoniae are an increasing public health threat in Tunisia, yet there is limited data on the circulating lineages and antimicrobial resistance (AMR) determinants underlying this threat. Here, we employed whole-genome sequencing (WGS) in the Tunisian AMR surveillance system (TARSS) to characterize the 3GC resistance mechanisms, population structure, virulence, and transmission across three participating sentinel hospitals in Tunis and Ben Arous. We sequenced a balanced sample of stored 3GCR (3GC-resistant) isolates from blood and urine collected between 2018 and 2022. Of 322 sequenced isolates, 286 (89%) were confirmed as K. pneumoniae , representing 28.5% of all stored 3GCR isolates. The population structure was diverse (68 sublineages) and distinct between hospitals, although several globally distributed sublineages were detected across sites (SL383, SL101, SL307, SL15). Extended-spectrum ß - lactamases (ESBL) genes were detected in 77% of genomes, with bla CTX-M-15 (65.4%) and bla CTX-M-14 (8%) dominant at all sites and across diverse sublineages. AmpC genes occurred in 9%, and carbapenemase in 19.6% ( bla OXA-48 , 14.7%; bla NDM-5 , 4.5%; bla NDM-1 , 3.8%), with carbapenemases mainly observed amongst SL147 and SL383 at Hospital B (41.7%). Despite sequencing less than a third of the unique 3GCR infections in each hospital, we identified 24 probable nosocomial transmission clusters involving 64 isolates. Each cluster was restricted to a single hospital, although many were detected across multiple wards in the same hospital. The acquired virulence-associated locus (ICE Kp ) encoding yersiniabactin was common (48.6%). Hypervirulence-associated markers (encoding aerobactin, salmochelin, and/or hypermucoidy) were rare (8.7%) but increasing over time. These were mostly found in sublineages in which convergence of ESBL and hypervirulence has been reported in other settings (including SL147, SL101 and SL383), suggesting international dissemination of convergent strains. These findings show sustained ward-level nosocomial transmission of 3GCR K. pneumoniae lineages and site-specific differences in ESBL and carbapenemase burdens, which call for targeted infection prevention and control and for future routine integration of WGS into TARSS.